A multi-omics approach to characterize the function of two RAP proteins essential for mitochondrial functions in the human malaria parasite, P. falciparum

The RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their biological functions remain unknown in the human malaria parasite, Plasmodium falciparum. In this study, we used inducible knockdown studies to show that PF3D7_0105200 (RAP01) and PF3D7_1470600 (RAP21) are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrated that these RAP proteins are involved in RNA metabolism and mitochondrial activity. Finally, using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validated that RAP01 and RAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs, indicating a role in regulating mitochondrial ribosome function. Collectively, our results establish the role of these RAP proteins in mitochondrial functions and contribute to further understanding of mitoribosome in malaria parasites.